May 16, 2024

Could you delineate a watershed and river network in 52 seconds? - Tutorial

May 16, 2024/ Saul Montoya

Delineation of watershed and river network is one of the most common tasks in modern hydrology but it might comprise a group of steps on a desktop software that take several minutes to perform. We wanted to recreate the process in an mostly automated workflow in an online platform that substantially reduces the amount of time involved in the process.

We came up with a solution on Hatari Utils (utils.hatarilabs.com) that allows us to delineate a basin of 530 km2 in just 52 seconds. Results from the platform also include the river network and the main river and are available as geospatial ESRI shapefiles.

May 11, 2024

ModelMuse version 5.2 has been released, explore what is new version.

May 11, 2024/ Saul Montoya

Even though that the version 5.2 was released on March 22 2024 we just found time to make a video explaning the new features of this version and where they are implemented on the graphical user interfase. This new version of Model Muse allows to simulate variable density and variable viscosity flow among other features of Modflow 6. Have a look on the video and wait for our comming applied tutorials related to these new features.

April 09, 2024

Land cover classification using a Naives Bayes algorithm with Python - Tutorial

April 09, 2024/ Saul Montoya

Machine learning can be applied to many fields as land cover classification from remote sensing imagery. The performance and accuracy of classification will depend on the number of raster bands, the image resolution, the land cover type and the algorithm used. This tutorial will perform an applied case of land cover classification from a panchromatic image in Python using the Naives Bayes algorithm implemented on the Scikit Learn package. The classification will cover four categories as: rivers, river beaches, woods and pastures; coding is performed under a Jupyter Notebook with Python running from a geospatial Conda environment. Some graphics and statistics about the classification precision are also included on the tutorial.

March 22, 2024

Simple example of ion exchange modeling with Phreeqc and Aquifer App - Tutorial

March 22, 2024/ Saul Montoya

An example that demonstrates the Phreeqc and Aquifer App capabilities to model ion exchange. This example uses the cation ion exchange approach where only the EXCHANGE keyword is used because EXCHANGE_MASTER_SPECIES and EXCHANGE_SPECIES are included in phreeqc.dat database. The model output is parsed as charts and tables and the solution composition and description are calculated and compared before and after the exchange.

March 21, 2024

A Python class to export Modflow 2005 model 3D geometry and parameters to Vtk - Tutorial

March 21, 2024/ Saul Montoya

Generating 3D visualizations of groundwater models is essential to analyze the flow regime, perform quality checks and see the interaction of the groundwater body with external factors / boundary conditions. The Flopy library has tools to export the parameters, boundary conditions and results that we have modified and compiled within a Python class. The use of this class allows the generation of Vtk files on a friendly way and in few steps. The tutorial also includes a representation of the parameters generated in ParaView.

March 18, 2024

Simple example of kinetic dissolution of calcite with Phreeqc and Aquifer Lab - Tutorial

March 18, 2024/ Saul Montoya

This is an example of calcite dissolution with kinetics where a simplified rate and initial molality are defined. The tutorial covers creation of an input file for Phreeqc, database selection, Phreeqc simulation in Aquifer App and analysis of processed output data on a Jupyter notebook. Finally the molality of Calcium and pH are plotted with time.

March 14, 2024

Interactive representation of a geospatial raster with Python, Folium and Rasterio - Tutorial

March 14, 2024/ Saul Montoya

Sometimes we want to reproduce or want to get something similar to a desktop GIS environment on a Jupyter notebook with options to show/hide layers and select background maps, but there was a missing part on our effort and it was the raster representation.

We have developed an applied case of single band raster representation on a Jupyter notebook with Rasterio and Folium. The raster has to be in WGS84 and the script can be coupled with more Folium features for the representation of vector data, background maps, menus and popups.

March 12, 2024

Simple example of irreversible reactions in Phreeqc and Aquifer App - Tutorial

March 12, 2024/ Saul Montoya

This is a tutorial of geochemical modeling in Phreeqc and Aquifer App that uses the REACTION keyword for the simulation of irreversible reactions that transfer a certain amount of elements to or from the solution. The selected example deals with the reaction of rainwater with NaCl and Calcite over 4 steps. Phreeqc simulation and model output analysis are performed on the Aquifer App that has great tools for the model setup and the analysis through interactive menus, tables and charts.

March 05, 2024

Simple example of mineral equilibrium in water with Phreeqc and Aquifer App - Tutorial

March 05, 2024/ Saul Montoya

This tutorial cover all the steps to build and run a geochemical model of a water sample in equilibrium with Fluorite and Gypsum. The tutorial explains the parameters to setup a mineral together with and analysis of the element concentrations, the amount of dissolved phases and the final saturation indices.

February 14, 2024

Automatic calibration of transient pumping test with MODFLOW 6, Python, FloPy and Scikit Learn - Tutorial

February 14, 2024/ Saul Montoya

Python has awesome packages for machine learning that can be coupled to groundwater models and perform automatic calibration of hydraulic parameters. This tutorial covers the procedure to implement a neural network based on a set of parameters set with corresponding head values; the study case is on a transient pumping test model with an observation point located around 10 meters away from the pump well. The analysis predicts the calibration parameters from the spatially interpolated observed head values.

February 13, 2024

How to export a MODFLOW 6 model grid to shapefile with Python and Flopy - Tutorial

February 13, 2024/ Saul Montoya

We did this tutorial since the documentation or examples on the topic were not available. Flopy can export the model grid and model attributes to shapefile with a coordinate system of reference for the three types of discretizations of MODFLOW 6. We have done an applied example to export the grid of a discretized by vertices model (DISV) to the ESRI Shapefile model. The tutorial also show options for the final grid representation in geopandas.

February 12, 2024

Seawater speciation modeling on cloud with Aquifer App and Phreeqc - Tutorial

February 12, 2024/ Saul Montoya

No more installations, no more database link up, no more raw text data as model output. Aquifer App now can run Phreeqc with great tools for the geochemical model setup, database selection and tables / graphics for the different simulation components.

This applied example calculates the distribution of aqueous species in seawater and the saturation state of seawater relative to a set of minerals and is based on the Example 1 of the USGS Phreeqc example documentation.

January 24, 2024

Sensibility analysis of transient pumping test with MODFLOW-6, Flopy and SALib - Tutorial

January 24, 2024/ Saul Montoya

This tutorial covers the whole procedure to perform a sensitivity analysis over a 72 hour pumping test plus recovery on the hydraulic response in an observation piezometer located at 11 meters from the well. the Since the study case it’s a transient model the sensitivities will vary over time and stage of pumping/recovery.

January 17, 2024

How to import a Leapfrog geological model to Model Muse with Python - Tutorial

January 17, 2024/ Saul Montoya

Having a geological model can enhance numerical models since it allows to represent higher accuracy the potential distribution of hydraulic parameters in the horizontal and vertical direction. The process to implement/insert a geological model into a Modflow model is a challenge due to restrictions on proprietary software and spatial tools; we have done the whole procedure to insert a geological model into a MODFLOW-NWT groundwater model with scripts in Python, Pyvista and others.

The code extracts the cell centroids of the modflow model and then compares its position with the different geological units exported from Leapfrog to Vtk. Once the corresponding lithology of the cell is identified a hydraulic parameter is assigned. The tutorial works from Vtks of a geological model done in Leapfrog, but it can work with any Vtk.

January 12, 2024

Convert geological units from Leapfrog (*.msh) to VTK using Python and GemGIS - Tutorial

January 12, 2024/ Saul Montoya

This tutorial shows the complete procedure to convert a geological unit as a Leapfrog mesh (*.msh) to the VTK (Visualization Toolkit) format using Python and GemGIS. Follow these steps to seamlessly transfer your geological data for advanced visualization, analysis and comparison with other model results.

January 11, 2024

Geological modeling of sedimentary layers from geospatial rasters with Python and Gempy - Tutorial

January 11, 2024/ Saul Montoya

Based on a coupled workflow on QGIS and Python it is possible to extract the required information for a Gempy model and run it for defined voxel sizes. This tutorial covers the whole procedure of spatial data preparation, data preprocessing in defined formats and geological modeling with Python and Gempy.

January 10, 2024

How to georeference a image/raster with Python and Rasterio - Tutorial

January 10, 2024/ Saul Montoya

Georeferencing in Python has the advantage that it can be performed repeatedly without the need to define control points each time. It also allows you to add/remove control points and observe the impact on the transformation array. This tutorial demonstrates the complete georeferencing process of a national map using 3 points whose pixel coordinates have been extracted from the Paint utility in Windows. The tutorial also exports the raster while assigning a reference system.

January 09, 2024

Groundwater modeling of a pumping test over a confined aquifer with MODFLOW-6 and FloPy - Tutorial

January 09, 2024/ Saul Montoya

We have done an applied groundwater model for a pumping test on a confined aquifer. The wellsite is located on the Clairborne aquifer (Georgia, USA) and has two observations on different layers besides the well itself. The aquifer test has two periods of pumping and recovery that last 3 days each one and the numerical model was constructed with MODFLOW-6 based on a Python script with the FloPy package. Comparison among observed and simulated wells were done with plots in Matplotlib.

December 04, 2023

Lithium speciation calculation on salt lake brines with Phreeqc and Python - Tutorial

December 04, 2023/ Saul Montoya

Lithium interaction with the aqueous phase on brines phase is not well understood or at least not well covered by the scientific publications. To evaluate brine composition, brine dynamics and the interaction of the different components is really a challenge with the available tools for geochemical modeling as Phreeqc since it doesn’t appear in all the databases and in most it is only associated with sulfates.

November 09, 2023

Online tools for groundwater modeling preprocessing with Model Muse - Tutorial

November 09, 2023/ Saul Montoya

If you want to speed up some steps in groundwater modeling you might be interested in the tools presented on this tutorial. We have developed some online tools that replace intense and time consuming tasks on desktop software and web servers and provide vector and raster data on the formats required by Model Muse. The tutorial covers the steps of DEM generation as Surfer Grid File (*.grd) with the definition of watersheds and river network based on two online services provided by Hatarilabs.

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